Problem importing BAM files in Artemis

[pasta]

Hi there,

My first post here and that will be a question.

We got data from the Illumina platform and I used BWA to align my reads on the reference genome, which generated BAM files at the end. I would like to visualize my data using Artemis but I cannot load my BAM file. Indeed, I receive this message :
"failed to open Organism.pe.bam.SORTED.bam: cannot recognise format of binary file"

I dont understand why ... The BAM file seems to be OK since I managed to open it with a bunch of different software.
I do have the latest version of Artemis+ACT+ Java, and I did index and sort my BAM file.

Any help would be appreciated.

Thanks

Toni

[pasta]

Forget abt my question - I just figured it out myself

(whaoo, it took me exactly 1 hour LOL)

[maubp]

And what was the solution? Anyone else with the same problem will probably find this thread via Google.

[Tani]

Ensure that the corresponding .bai file in the same directory as of .bam file

[pasta]

I just did something stupid with Artemis... I tried to load the BAM file straight away without any genome loaded first .... I thought it was worth mentioning I was stupid LOL

[Trudy]

How do you solve this problem?
I have the same problem..Could you help me?

ARTEMIS doesn't load my bam file..
I sorted and indexed the file.bam with samtools.....but the problem persist!

help me please....

[pasta]

How do you solve this problem?
I have the same problem..Could you help me?

ARTEMIS doesn't load my bam file..
I sorted and indexed the file.bam with samtools.....but the problem persist!

help me please....

Well, first load your Genbank file(s) on the startup window:
File > Open > select your files
Then, when your chromosome is loaded, on the new window simply choose:
File > Read BAM/VCF > select your file

Hope it helps !

Toni

[coldturkey]

I don't have a problem opening bam and vcf files in artemis, however, I would like to open multiple vcf files at the same time so they can be viewed in separate rows in the vcf panel.
I have supplied artemis a file contiaing the full paths to each vcf file (as per instructions on the artemis website) but only one vcf file is displayed. Has anyone tried to do this?

regards

Brian